Mystery Agent
by Jess Marylin
Summary: After the events of Iron Man 3, Director Fury assigns a previously unknown agent for a completely Top Secret Mission. This agent has a mind of her own, and a past that is a complete mystery to her. Just who is Agent Lynx? Tony/Pepper. Major spoilers for Iron Man 3, you have been warned.
1. Chapter 1

_**The Avengers doesn't belong to me. Just my OCs. :)**_

_**Anywho, big warning. Major, I repeat, major spoilers for Iron Man 3. If you haven't seen it yet, well, you've been warned...**_

* * *

**10:15am, January 25th, 2003. Undisclosed location.**

The teenager looked around in utter confusion as three black-suited men, who looked very much like FBI agents even though she knew that they weren't, led her down a well-lit hallway. She was tempted to believe that they were leading her to her death like in the horror movies, but she knew better. The man leading the group, the one with friendly features and the only one of them currently not wearing sunglasses, had personally promised her that none of them would so much as touch her. So far, his promise was being kept.

That made sense to her though. The Professor had insisted on reading their minds before he would even consider letting her go with them. Once the telepath had been sure that she would be safe and that the Agents were telling the truth, he had left the decision up to her.

It had been the fourteen year old's decision to go with the men. They'd all climbed into a big black SUV and had driven about two hours by the time they'd reached what looked to be a military airbase.

Without hesitating, they'd led her to a weird looking helicopter. Instead of the blades being on top and at the tail, this one had blades in the center of each of it's wings. It was more like a cross between a helicopter and a plane. The kind looking guy took a seat next to her as his two subordinates took the seats behind them.

As soon as they'd safely strapped in, the helicopter/plane took off and the girl clenched her armrests so tightly that her knuckles turned white.

"You've never flown before, have you?" Kind Guy had asked with a hint of concern in his tone.

She'd shook her head while trying to force herself not to hyperventilate, "When you said it wasn't that long of a trip, I wasn't exactly expecting a plane ride." This was only her first time, but she had already quite decided that she really, _really_ hated flying. "If people were meant to fly, we'd have wings," she'd trailed off, biting her lip to keep the nausea at bay.

The man beside her had chuckled softly at that.

After they'd disembarked, the four of them had kept a brisk pace across the landing zone atop of what appeared to be a huge aircraft carrier. And now, halfway down the well-lit hallway, the two sunglass wearing Agents branched off, leaving her with Kind Guy. Even though she knew that those men hadn't meant her any harm, she felt a sense of relief that they weren't tailing her anymore. Looking back and not being able to see their eyes had been very unnerving.

Kind Guy stopped at one of the many doors and placed his thumb on a pad by it. The door swished open, revealing a dark-skinned, bald man sitting at a table, an empty chair across from him. The girl froze in the doorway, her hazel eyes fixed on the sitting man's eyepatch. Kind Guy placed a hand on her shoulder and gave a gentle, reassuring squeeze.

She looked up at him, but his gaze was focused on the one-eyed man, "Is there anything else, sir?"

The man rose from his seat, "No, Coulson, you're dismissed."

Casting one more reassuring glance her way, Coulson disappeared down the hallway.

Bald Guy motioned for the girl to take the chair, and she nervously did so. Once she was seated, he resumed his own seat, "My name is Director Fury, of S.H.I.E.L.D. And, according to my sources, you are known as Lynx, correct?"

"Yes, sir," the teenager responded, hating how small her voice sounded.

Director Fury acted as if hadn't even noticed that her voice had quivered, "Lynx, my sources also say that you have quite a few remarkable abilities. Is that so?"

"Yes, sir," Lynx responded again, proud now that her voice hadn't shaken that much the second time around.

"Well then. Lynx, I believe that we may have a proposition for you..."

* * *

**10:15am, January 25th, 2013. S.H.I.E.L.D. Helicarrier, undisclosed location. One month after the destruction of Tony Stark's Iron Man suits.**

Lynx stood, looking at the very spot were Agent Coulson, always 'Kind Guy' in her mind, had fought his last fight. If only she'd been there, Loki would not have _dared_ attack him. In fact, _if_ she had been present at the time when the wicked Asgardian had escaped, he might not have escaped at all. _At least not alive._

She realized that today was exactly ten years to the day that Phil himself had brought her aboard the Helicarrier to meet Fury. _Exactly_ nine years. She'd planned to meet with him again today and talk about old times since they hadn't seen each other since her training had been completed a year ago. And now, she was staring at the very spot where he'd _died_. Any evidence of the fight that had ended his life had long since been cleaned up, but she could still smell the sickening scent of blood. _Phil's blood._ Tears sprang to her eyes and she fought to keep them at bay.

_If only I had been here._ But no, Fury had sent her halfway across the world on another mission several days before Loki's arrival via the Tesseract. Lynx had even been too far away to reach New York in time to help the Avengers during the Chitauri Invasion, as not a single Quinjet could be spared to pick her up. _Though I'm getting the feeling that Fury really didn't want me to become part of that team._

What pissed her off though, wasn't that she hadn't been able to help. Her lack of transport had been totally out of anyone's hands. What royally angered her was that Director Fury had neglected to inform her that her former mentor had been murdered until today, which was _months_ after the fact. Of course, One-Eyed Pete claimed that he'd simply been too busy. _Too busy to keep one of his top Agents in the loop? Bloody likely._

Her sharp ears caught the sounds of said man's boots approaching her from behind. Fury stopped about five feet away, but Lynx didn't turn to face him. She still refused to acknowledge him when he gave a soft sigh to announce his presence.

At least Fury knew well enough to not venture moving closer to her. He knew what she was capable of, especially when she was this pissed.

Lynx let him stew for a few minutes before finally addressing him, all the while keeping her eyes on the spot were Phil's blood had once been smeared, "What now, Director? Come to tell me something else you've conveniently forgotten over a nice cup of sweet tea?"

"I actually came here to apologize."

So stunned was she, that she whipped around to face him, her eyes _almost_ shifting. "_Apologize_? The great Nicholas Fury, the mighty Director of the Strategic Homeland Intervention, Enforcement, and Logistics Division himself coming to apologize for simply being busy?" she snapped back, her already pronounced Southern accent coming out heavier with her irritation.

"Almost as bad as Stark," he mumbled, still unaware of just how acute her hearing really was. And she preferred to keep him in the dark when it came to the true extent of her abilities. When she was younger, she'd had no reason to hide anything from S.H.I.E.L.D. But, as she'd matured, she'd learned that the less they knew, the less control they had over her life.

He sighed again, heavier this time, "I realized that I should have told you sooner, Lynx, and I regret not doing so. However, there are more important things-"

This time, her eyes did shift. Her irises enlarged until there was no white to be seen and changed to a dusky yellow. Her pupils became slits as she stared right back at him, "Something more important than giving me time to grieve for my friend? Do you not realize that Phil was the only one I ever really trusted in this entire bloody Division?!"

"The emotions of one being are nothing compared to the well-being of the entire planet," Fury snapped back at her, not even fazed by her threatening eyes. "You _know_ that, Agent Lynx."

_All I know is that you're a pompous big-head who is always right, no matter what._ But voicing that opinion was treading on thin ice and Lynx knew it. She brushed stray black curls away from her oval-shaped face. "I do." _I do know that's what _you_ think. But I don't believe it. How can you fix the bigger picture if you're not focusing on the little things too?_

Fury went on as if there was nothing more to discuss, "As it is, you're going to be late for your next mission."

_Yes, your Royal Haughtiness. Anything thing else, Your Excellent Big-Headedness?_

* * *

_**As you can see, Agent Lynx has somewhat of an attitude problem. As for who she really is... well, you'll just have to keep reading to find out.**_


	2. Chapter 2

_The Avengers does not belong to me. Just Lynx._

_Big thanks to Vadersfist501st and Aureus Lux for reviewing!_

_Again, major spoilers for Iron Man 3. Just sayin'._

* * *

**11am, February 8th, 2013. Stark Industries, New York City Office.**

Lynx sat quietly, awaiting an interview with Pepper Potts. The last receptionist for the CEO's office in New York had conveniently been offered a higher-paying government job. And, also conveniently, most of the other applicants had gotten the wrong date for their interviews, which left three currently Stark Industries employees sitting in the lounge. The first was a sharp looking caramel-skinned woman, the second was a timid-looking man, and the last was a petite girl with black curls, who was Lynx herself. As the caramel-skinned woman was called in for her interview, Lynx checked her hard-copy resume and application again, as if worried that she'd forgotten something, then set the papers back into her lap while composing her face into a relieved mask as if she'd found out that everything was in order.

Stark Industries' newly appointed head of security, a recently recovered Mr. Hogan, eyed Ms. Potts' possible receptionists with open suspicion from his seat across the room. _That guy certainly doesn't do subtle._ Lynx was pleased to see that Hogan was focusing on the man, who'd just dropped one of his papers for the hundredth time. She fought to keep a smile back and failed, just managing to look down at one of the magazines on the table next to her when Hogan's unrelenting gaze swept over her.

Even though it appeared that she was choosing which magazine to look at while she waited, Lynx was actually listening to a conversation happening behind one of the solid wood doors. One man's voice was reiterating a sequence of events that had happened to him while the other man's breathing deepened in sleep. As soon as he'd gone about five minutes more into the narrative, she instantly recognized him as Tony Stark. As for the sleeping man, she had no clue who he was, but that didn't matter to her. As far as she knew, Mr. Stark wasn't supposed to be at the office at all. _But, then again, Stark's never really been predictable anyway._

She listened as he explained everything about the Extremis project and his fight with Aldrich Killian in Miami, apparently not noticing that his audience of one was still snoozing or that he had an eavesdropper. Most of the info she'd read on S.H.I.E.L.D.'s reports, but several things she hadn't heard. Like the little boy named Harley in Tennessee. If she had been younger, Lynx didn't doubt that she would have immediately reported everything back to headquarters, but she was twenty-four now and nowhere near as stupid. Fury had no business knowing about the little boy who had helped Stark when his suit had died on him.

So focused was Lynx on the one-sided narrative, that she hadn't noticed Mr. Hogan calling her false name. She finally heard him approach, but waited until he was standing right in front of her before looking up at him in fake shock. "Didn't you hear me, Ms. Taylor? That is your name right? Aliya Taylor?"

"Mrs., actually. I'm sorry, I was so focused on trying to make sure I had my references straight that I-"

He waved his hand, clearly not concerned anymore that she could have been up to something, "My bad, Mrs. Taylor. Ms. Potts is waiting on you."

That was when one of the wood doors down the corridor opened and a somewhat irritated Stark exited with a sleepy Bruce Banner following behind him. Lynx stared at Stark for a moment longer than was necessary, acting the part of a young woman who has caught sight of some celebrity before shaking her head as if making herself focus.

_First the interview. Then you can start figuring out how in hog heaven you're gonna gain Stark's trust._

_Well, if Agent Romanoff did it, then so can I. I just hope nobody hates my guts when all the crap finally hits the fan. I should have been more stubborn about doing this my way instead of giving in to Fury so easily._

* * *

**12 noon, February 13th, 2013. Stark Industries New York Office.**

"Stark Industries, one moment please," Lynx answered the phone calmly, putting the caller on hold before switching back to another line. "I'm sorry sir, but Ms. Potts is in a meeting at the moment may I take a message? No, I'm afraid Mr. Stark isn't in either, but I can take a message." Just as she was about to pick up the pen, the phone rang again, "One moment, sir, and I'll be right back with you. Stark Industries, how may I help you?"

"You can help by telling me how you got so good at answering phones like that, Ms. Taylor." _Speak of the devil._ Stark was standing right in front of her and she hadn't even heard him come in. Come to think of it, she hadn't caught his scent either. _I can't get complacent like that again. Lucky for you, Lynx, it was Stark who sneaked up on you this time and not an enemy._

Lynx held up her finger in the universal signal of 'one moment' as she commenced to wrap up all three calls. Just as she was about to answer the billionaire in front of her, the phone rang again, but as she reached for the receiver, Stark motioned for her to leave it. Which earned him a weird look from her. "Have you ever heard of 'lunch break'?"

"If Miss Potts works through hers, so can I," she responded politely, her fingers twitching toward the still ringing phone. "And it's _Mrs._ Taylor," she corrected, holding up her left hand so that he could see her ring.

Stark took her distraction as an opportunity to slide the entire phone away from her with one hand as he shook his finger at her, "Well, you're not going to, Mrs.- You know what, how about I just call you by your first name? Aliya's definitely less of a mouthful than Mrs. Taylor. By the way, you're kind of too young to be married."

"Early twenties isn't too young, Mr. Stark," Lynx answered, still looking longingly at the now silent phone that was just out of her reach.

"Okay... But you still haven't answered my first question, Aliya. You know-"

"I remember, sir. I used to be a salon receptionist, once upon a time."

"And what's with the all the 'sirs'. And where did you learn that ridiculous accent?"

Lynx pretended to take offense. After all, a lot of people did when Stark decided to pick on them. "For your information, _sir_, I was born and raised properly in the South and we don't take kindly to being picked on for the way we talk. That, and my momma would tan my hide for showing anything less than proper respect for a superior. _Sir_."

That, surprisingly, got her a chuckle from Stark. But, before he could say anything further, Pepper Potts herself exited her office, "Tony, quit bothering Aliya. She's the best we could have gotten and I don't need you scaring her off."

_Oh, don't worry, Potts. I don't scare so easily._

Stark ducked his head sheepishly and Potts turned her attention to Lynx, "And what are you still doing here, Aliya? It's already ten after."

Lynx opened her mouth to answer, but Stark beat her to the punch, "She said that she likes to work through lunch." He looked to her, a mischievous smile on his face. _I'm getting the feeling that I'm gonna pay for that 'sir' tirade. _"You're not anorexic, are you?"

"Anthony Edward Stark!" Pepper admonished harshly, a mortified expression on her face.

Lynx just calmly looked back at Stark before bursting out laughing.

* * *

**1pm, February 20th, 2013. Currently being renovated Stark Tower, Stark's private floor.**

Thanks to her being able to handle Stark's annoying personality, Lynx found herself being trusted to run files to Stark at his tower, as he was currently trying to ignore anything work related at the moment. Even though Potts was CEO, she still had a few folders of paperwork that needed his approval. And since Potts was needed at the office, it was up to Lynx to make sure that the man at least _reviewed_ the papers. Granted, she had to do it on her lunch break, but that hardly mattered to the agent. What mattered was that she was finally getting a good look at Stark Tower, and that was extremely important for her mission.

Lynx held said papers protectively to her chest as she prepared to enter Stark's workshop. Since he'd destroyed all of his Iron Man suits via J.A.R.V.I.S.' clean slate program, he'd begun tinkering with other things that she couldn't even begin to explain. But she could tell that his current project was a miniaturized version of the already miniaturized ARC reactor that used to be implanted in his chest. _Another little gadget for his company, I guess._

She winced as she pushed the door open, resisting the urge to growl in annoyance at how overwhelmingly _loud_ his music was. "MR. STARK!"

He jumped at her bellowing his name, telling his computerized butler to mute his music before turning to her, "What's with all the yelling, Aliya?"

Lynx handed him the papers, her hands finally free to rub her now throbbing ears, "How in God's green Earth can you still hear after listening to that caterwauling, Mr. Stark?"

"There's nothing wrong with ACDC," he answered, on the offense.

"Of course not, sir. I love their music too. But, in Live Oak, we're not really used to loud music like that. My ears'll be ringing 'til kingdom come."

"Live Oak?"

"Florida, we're I'm from." That much at least was true. The Professor had found her wandering the swamplands around the small town and had brought her back to the Institute where she'd grown up. But that was strictly classified intel. As to how she'd ended up on her own in alligator country... Well that was still a mystery to her.

* * *

_Please R&R._


	3. Chapter 3

_The Avengers do not belong to me. Just Lynx._

_Big thanks to everyone who took the time to read this little story!_

* * *

**10pm, February 20th, 2013. Times Square.**

Over the past several weeks of her employment, Lynx had taken patrolling the area around Stark Tower for at least several hours each night. Not a sign of anyone coming after Stark, now that he was no longer Iron Man. Which, so far, meant that her mission was pointless. Fury had assigned her to watch over Stark and Potts, now that the Armored Avenger had apparently given up on being a superhero.

_It looks like the bad guys aren't interested in him anymore either, since he's not really a threat to them now._

With her mission seemingly turning out to be a flop, Lynx had tried to find other ways to occupy her time while still keeping an eye out for any possible threats to Stark. She'd ended up doing plain old vigilante work. Shoot, she'd even caught a glimpse of Spider-Man a once or twice, but since he wasn't a threat to anyone unless they were criminals, she'd let him be. Fury was still giving her grief over that decision. _But he's not the one out here on the field. Spidey seems to be doing good on his own and I will not bring S.H.I.E.L.D. down on his head so that they can assimilate him too._

Thanks to her abilities, fighting average criminals took her no time at all and it wasn't long before she found herself back right where she'd begun the night. At the Broadway theater that Stark and Potts had gone for their date night. His car was still in the parking lot, so it was safe to assume that they hadn't left yet.

Lynx sniffed the air, checking for anything out of the ordinary when she caught a familiar scent. She couldn't quite place it, but she _knew_ that she'd smelled it at least once before. She sniffed again, but the scent was gone. Normally, she wouldn't have been too concerned, but now she couldn't help but be worried. Just that hint of a scent had been enough to cause her to go on high alert and that meant that something definitely wasn't right.

The sound of Potts laughter had her focusing on the entrance to the theater below her. It seemed that the show was over. Stark, Potts on his arm, was walking towards his sports car. Judging by the way the man had his mouth to the woman's ear, he was whispering something about how the two of them should 'turn in for the night'. Lynx rolled her eyes, thanking her lucky stars that, even though her hearing was good enough to pick up his voice from this distance, it wasn't acute enough for her to actually discern whatever Stark was whispering. _Oh well. At least I can count on the both of them being at the Tower until the morning._

As she followed couple via the rooftops, she couldn't help but think about that scent. _I have a bad feeling that I'll be meeting whoever it belongs to very soon..._

**12am, February 21st, 2013. Lynx's Chelsea apartment.**

"Well, I'm sorry you feel that way, sir. But since I was the agent on the ground, the call was mine to make."

"_You don't get to make the decisions, Lynx. You _know_ that we need to talk to the kid. We don't know who's side he's really on and you're the only agent I've got who's even capable of taking him in._"

"With respect, Director, when you say 'need' all I hear is 'want'. And I thought actions spoke louder than words? If so, Spider-Man's actions, past and present, speak volumes. He's a good kid and I ain't going after him. Forget it."

"_Agent-_" Fury began again, a tone of warning in his voice.

"Don't 'Agent' me, Nick. I may work for you, but you don't own me. I'm not a soldier you can order around. But I _am_ an honorary X-Man and, as such, I'm not even completely under your authority."

"_And now you're on _very_ thin ice, Lynx._"

"Maybe if you hadn't kept me in the dark about Phil, we wouldn't be having this conversation. Now, if you'll excuse me, sir, I've gotta go. As you're well aware I've got to be at SI at 9 and I don't plan on working on no sleep just because you've got your panties in a knot over something stupid."

"_Lynx-_" Said woman shut off her cell, effectively cutting off whatever it was that Fury had been about to say to her.

"I don't care what you think, Fury. You know as well anyone that I'm going to do what I know to be right. And I'm not going to let anyone, including you for that matter, try to stop me." She angrily threw the cell onto her floor, giving it one good glare before laying down on her bed and firmly turning her back on it. Lynx wasn't worried about Fury trying to call her back, he'd learned by now that it wouldn't get him anywhere.

But, as if to prove her wrong, the phone went off again.

"This had _better_ be worth it. Hello?"

"_Just thought you should know that I made it back safely_," a man's voice, but this time one with a slight Irish accent, greeted her.

"Carter?" she gasped, nearly dropping the phone in her surprise. "I thought you weren't getting back until next week?"

"_We finished early, love. I won't be back in the states for a few hours yet, but I had to call you. I love you, and I'll see you later today, alright?_"

"Alright, love you too. And you'd better not take your time, O'Riley. You hear me?"

Carter chuckled, "_Wouldn't dream of it._"

There was a click and Lynx found herself much to excited to even try to sleep. Carter was coming back! She hadn't seen him for months and missed him more than she could ever explain. _Just a few more hours and he'll be in my arms!_

**11am, February 21st, 2013. Stark Industries Main Office. New York City.**

Lynx jerked as someone snapped their fingers in her face, her eyes focusing on the steaming cup of coffee the same someone had apparently just placed in front of her. She blushed, ashamed. _It's not like me to phase out like that. _But, because of her excitement about O'Riley's impending return she'd gotten no sleep the night before. That wouldn't have been an issue if the man wasn't the only one who caused her to daydream, which was why Potts was again snapping her slender fingers in Lynx's face. She fought back the urge to growl in annoyance and simply looked up, wide-eyed, at her boss.

"Figured you could use a pick me up, Aliya. Care to tell me what's going on?"

"Ms. Potts? Oh my gosh, I'm so sorry! How long have I been out of it?"

Potts laughed lightly, "Long enough for Tony to give up on trying to get your attention."

_Stark was here? Oh dear lord, I'm never gonna hear the end of this!_ Lynx felt her blush deepen as she mentally berated herself. _I'm supposed to be on my guard, not daydreaming about my man!_ "I'm so sorry, Ms. Potts," she said again. "I didn't mean to phase out like that, it's just that I got a call from my husband last night."

"Is everything alright?" Potts asked, concern on her face. That was when the phone rang and Lynx reached for it, but the older woman motioned for her to leave it. "Aliya?"

Lynx nodded, "Yes, ma'am. Never better, actually. He's just on leave earlier than we expected."

"So, you really were telling the truth, huh Zombie Girl?" That was Stark. Lynx rolled her eyes, _I must have _really_ been out of it for him to call me something like that._ "When's soldier boy getting back?"

Lynx smiled widely, but she wasn't looking at either of her bosses. Rather, she was looking _behind_ them. Carter was standing in the doorway, dressed in his camo fatigues and combat boots. And grinning like a fool at her. He was earlier than she'd thought, but what did that matter? He was home, he was safe and she was close enough to actually catch his scent... which caused her to blanch.

Because it wasn't Carter that was smiling back at her. It wasn't O'Riley that Stark and Potts were turning to greet. The scent she caught coming from the man in the doorway wasn't Carter's. Carter's scent was the distinctly masculine scent of sweat, motor oil, and, oddly, pine. This person's scent was nothing at all similar, as it was cloyingly sweet. Lynx found herself reaching for the concealed pistol that Fury had forced her to carry for this mission.

Carter's doppleganger's smile faded somewhat and the eyes flashed yellow for a second. Much too fast for either Stark or Potts to catch. Not even Hogan, who was sizing up the newcomer from his usual corner, caught it. But Lynx did.

Mystique, looking at her with Carter's face, frowned.

_What the hell? I thought she was in Ravencroft? She's not even supposed to have her powers!_

But that wasn't what had her unsettled. What scared her was that Mystique had come to her in Carter's form and that the shapeshifter was ignoring everyone but Lynx herself.

_If she's laid one finger on my man, I'm gonna rip her to shreds!_

And, of course, the three other people in the room were completely unaware that they were facing a wolf in sheep's clothing. And a deadly one at that.

* * *

_Oh, and did I mention that Spider-Man and the X-Men don't belong to me either? ;)_

_Please R&R._


End file.
